I did a bit more research on the Ferrari 330 P4 in general.
The car that's been in the series since Gran Turismo 5 in 2010 is CN.0858. It started off as a berlinetta, converted to a spyder for Brands Hatch '67, then further converted into a Can-Am racer. However, despite being portrayed as a spyder since Gran Turismo 5, it was converted to a berlinetta some time after its time as a Can-Am racer - specifically at some point between 2009 and 2014. Indeed, I cannot find any photos of CN.858 as a spyder at the likely time where PD would be working on GT5, as circa the late 00s, it was still a Can-Am racer. Of course, PD could have used historic information to recreate CN.858 as it was when it went to Brands Hatch in '67, sort of like how I recall hearing that the iconic Suzuki Escudo Pikes Peak Special no longer exists in the form we're most familiar with.
Meanwhile, the 330 P4 that won the 2016 Pebble Beach Trophy is CN.0856. Like CN.0858, this one also started off as a berlinetta and was converted to a spyder for Brands Hatch '67. However, unlike CN.0858, this car remains a spyder to this day, with no changes made to it afterwards. Although its current number sticker is 7, it formerly ran as car #24, taking second at the 1967 Daytona 24h and third at Le Mans that same year. Furthermore, it's previously had some high-profile owners like Bernie Ecclestone and Lawrence Stroll. Despite the official Gran Turismo page
stating this was the car that took second at the 1967 24 Hours of Le Mans, that honor goes to CN.0858. (Notably, CN.0858 was a berlinetta at Le Mans, not a spyder.) Furthermore, having access to a 330 P4 spyder today could allow PD to get more accurate information on the 330 P4, rather than relying on historical records.
Therefore, it seems likely that CN.0858 will be entirely replaced with CN.0856 in the next Gran Turismo title.
There's also CN.0860, which is indeed a spyder today, but unlike CN.0856 - and more like CN.858 - it was also converted to a Can-Am racer. In the early 70s, it was then changed back to a spyder.